It's interesting that you mention that - in light of the assortment of things that have been tweaked in the new firmware, I've been tinkering around with some testing to see how it behaves when surround modes change, and I think the behavior you describe has been resolved. My test was to have an input of a certain type, assign it to a processing mode, and then have a series of events that would cause it to re-acquire the original source (pause a DVD, go into the menu and back out, change inputs to a different format, turn the 990 off and back on, ...) - I haven't seen PCM behave that way in these tests.
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gonk
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